Multiple sequence alignment - TraesCS7A01G413200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G413200 chr7A 100.000 5155 0 0 1 5155 603960434 603955280 0.000000e+00 9520.0
1 TraesCS7A01G413200 chr7A 86.207 1450 160 16 207 1653 603945198 603943786 0.000000e+00 1533.0
2 TraesCS7A01G413200 chr7A 86.402 831 107 5 766 1593 603025373 603026200 0.000000e+00 904.0
3 TraesCS7A01G413200 chr7A 85.760 625 75 10 87 709 603024589 603025201 0.000000e+00 649.0
4 TraesCS7A01G413200 chr6A 95.238 2436 67 10 2739 5155 26782087 26779682 0.000000e+00 3810.0
5 TraesCS7A01G413200 chr4A 96.005 1677 45 12 1669 3323 614703078 614701402 0.000000e+00 2706.0
6 TraesCS7A01G413200 chr4A 96.964 1515 45 1 3641 5155 614701355 614699842 0.000000e+00 2542.0
7 TraesCS7A01G413200 chr7D 93.985 1646 85 3 2 1639 523437255 523438894 0.000000e+00 2479.0
8 TraesCS7A01G413200 chr7D 86.355 1517 152 25 116 1627 523277258 523275792 0.000000e+00 1604.0
9 TraesCS7A01G413200 chr7D 84.669 1572 200 24 3 1563 522872686 522874227 0.000000e+00 1530.0
10 TraesCS7A01G413200 chr7D 83.962 848 132 4 766 1611 523269158 523268313 0.000000e+00 809.0
11 TraesCS7A01G413200 chr7D 85.117 383 43 3 116 498 523486508 523486876 3.770000e-101 379.0
12 TraesCS7A01G413200 chr7D 100.000 28 0 0 1589 1616 523488545 523488572 9.000000e-03 52.8
13 TraesCS7A01G413200 chr7B 94.106 1561 78 3 102 1653 558642057 558640502 0.000000e+00 2361.0
14 TraesCS7A01G413200 chr7B 85.515 1650 168 36 3 1648 558365224 558363642 0.000000e+00 1657.0
15 TraesCS7A01G413200 chr7B 85.078 1595 204 24 3 1593 556687500 556689064 0.000000e+00 1596.0
16 TraesCS7A01G413200 chr1A 93.596 1093 69 1 4063 5155 298122587 298123678 0.000000e+00 1629.0
17 TraesCS7A01G413200 chr4B 75.664 226 47 6 236 457 483698552 483698773 7.060000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G413200 chr7A 603955280 603960434 5154 True 9520.0 9520 100.0000 1 5155 1 chr7A.!!$R2 5154
1 TraesCS7A01G413200 chr7A 603943786 603945198 1412 True 1533.0 1533 86.2070 207 1653 1 chr7A.!!$R1 1446
2 TraesCS7A01G413200 chr7A 603024589 603026200 1611 False 776.5 904 86.0810 87 1593 2 chr7A.!!$F1 1506
3 TraesCS7A01G413200 chr6A 26779682 26782087 2405 True 3810.0 3810 95.2380 2739 5155 1 chr6A.!!$R1 2416
4 TraesCS7A01G413200 chr4A 614699842 614703078 3236 True 2624.0 2706 96.4845 1669 5155 2 chr4A.!!$R1 3486
5 TraesCS7A01G413200 chr7D 523437255 523438894 1639 False 2479.0 2479 93.9850 2 1639 1 chr7D.!!$F2 1637
6 TraesCS7A01G413200 chr7D 523275792 523277258 1466 True 1604.0 1604 86.3550 116 1627 1 chr7D.!!$R2 1511
7 TraesCS7A01G413200 chr7D 522872686 522874227 1541 False 1530.0 1530 84.6690 3 1563 1 chr7D.!!$F1 1560
8 TraesCS7A01G413200 chr7D 523268313 523269158 845 True 809.0 809 83.9620 766 1611 1 chr7D.!!$R1 845
9 TraesCS7A01G413200 chr7D 523486508 523488572 2064 False 215.9 379 92.5585 116 1616 2 chr7D.!!$F3 1500
10 TraesCS7A01G413200 chr7B 558640502 558642057 1555 True 2361.0 2361 94.1060 102 1653 1 chr7B.!!$R2 1551
11 TraesCS7A01G413200 chr7B 558363642 558365224 1582 True 1657.0 1657 85.5150 3 1648 1 chr7B.!!$R1 1645
12 TraesCS7A01G413200 chr7B 556687500 556689064 1564 False 1596.0 1596 85.0780 3 1593 1 chr7B.!!$F1 1590
13 TraesCS7A01G413200 chr1A 298122587 298123678 1091 False 1629.0 1629 93.5960 4063 5155 1 chr1A.!!$F1 1092

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
253 269 0.319555 TCGTCTTGTTTCTCGGCCTG 60.320 55.0 0.0 0.0 0.00 4.85 F
1531 1684 0.176680 TCTGGATCGCTTCTTCTGGC 59.823 55.0 0.0 0.0 0.00 4.85 F
1845 3077 0.249911 GAAGCACCTTCCTCGTGTGT 60.250 55.0 0.0 0.0 34.71 3.72 F
2662 3916 0.331278 CCAACACCCCTGCAATCCTA 59.669 55.0 0.0 0.0 0.00 2.94 F
3224 4478 0.394899 CAAGAGGGGTCTGGCAATCC 60.395 60.0 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3215 0.321671 GCTGGAGGTGTCAGTAAGCA 59.678 55.0 0.00 0.0 34.89 3.91 R
3357 4630 0.106149 AACGACAGGGACAACACCTC 59.894 55.0 0.00 0.0 35.78 3.85 R
3416 4689 0.964358 AGACCCCGTACGTTCCAGAG 60.964 60.0 15.21 0.0 0.00 3.35 R
3884 5157 0.865769 ATGAACCGACGAAACACAGC 59.134 50.0 0.00 0.0 0.00 4.40 R
4769 6042 0.035317 AGAAGTGCGCAGTGAATCCA 59.965 50.0 20.39 0.0 0.00 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.378728 TCAATTAATTACGATACTCTGCAGTCG 59.621 37.037 19.40 19.40 39.78 4.18
63 72 4.298744 GCCTGGAGCACTTCAATTAATC 57.701 45.455 0.00 0.00 42.97 1.75
75 84 8.792538 GCACTTCAATTAATCGAGAAAATTCAG 58.207 33.333 0.00 0.00 0.00 3.02
78 87 9.219497 CTTCAATTAATCGAGAAAATTCAGAGC 57.781 33.333 0.00 0.00 0.00 4.09
79 88 8.267620 TCAATTAATCGAGAAAATTCAGAGCA 57.732 30.769 0.00 0.00 0.00 4.26
120 131 6.097915 TCGTTAGAATTTGGTCTCTCTGTT 57.902 37.500 0.00 0.00 0.00 3.16
190 201 2.804090 GTCGAGAACGGCGTGTCC 60.804 66.667 15.70 6.24 40.21 4.02
191 202 3.289062 TCGAGAACGGCGTGTCCA 61.289 61.111 15.70 0.00 40.21 4.02
253 269 0.319555 TCGTCTTGTTTCTCGGCCTG 60.320 55.000 0.00 0.00 0.00 4.85
331 347 3.164011 CAGTTCGACGACGGCGAC 61.164 66.667 28.04 20.23 41.64 5.19
392 408 0.587768 CGTGTTCAACATGAGCTGCA 59.412 50.000 3.37 0.00 37.29 4.41
643 659 1.338337 CTCTACGACATGCCGGAAGAT 59.662 52.381 5.05 0.00 0.00 2.40
664 680 1.450312 CCTCGCCATGAAGGGTGTC 60.450 63.158 0.00 0.00 39.49 3.67
753 888 3.030291 TGCTTGGTTCAATTCACCACTT 58.970 40.909 5.63 0.00 44.34 3.16
802 937 4.344968 TGATCAGATTCTTCGATAAGGCCA 59.655 41.667 5.01 0.00 33.22 5.36
837 972 1.461268 TGACAAGGAGGTGGAGGCA 60.461 57.895 0.00 0.00 0.00 4.75
982 1117 1.472480 TGCAGATCTCGTCGACATTCA 59.528 47.619 17.16 0.00 0.00 2.57
1101 1236 1.461559 CTCTCTACGACCGGGTCTTT 58.538 55.000 23.86 13.50 0.00 2.52
1113 1248 2.975799 GTCTTTGTTCCGGCGGCA 60.976 61.111 23.83 7.99 0.00 5.69
1159 1294 2.132996 ATCTCGGAGCTGCAGAGGG 61.133 63.158 20.43 5.12 39.04 4.30
1531 1684 0.176680 TCTGGATCGCTTCTTCTGGC 59.823 55.000 0.00 0.00 0.00 4.85
1628 2860 6.479990 GGTTGCTGATTTTTAAGTTGCTTCTT 59.520 34.615 0.00 0.00 0.00 2.52
1629 2861 7.339953 GTTGCTGATTTTTAAGTTGCTTCTTG 58.660 34.615 4.66 0.00 0.00 3.02
1648 2880 4.706476 TCTTGGTGGGCAGAGATATTTTTG 59.294 41.667 0.00 0.00 0.00 2.44
1653 2885 2.428171 GGGCAGAGATATTTTTGCAGCA 59.572 45.455 10.42 0.00 38.27 4.41
1654 2886 3.490419 GGGCAGAGATATTTTTGCAGCAG 60.490 47.826 10.42 0.00 38.27 4.24
1655 2887 3.129988 GGCAGAGATATTTTTGCAGCAGT 59.870 43.478 10.42 0.00 38.27 4.40
1656 2888 4.381292 GGCAGAGATATTTTTGCAGCAGTT 60.381 41.667 10.42 0.00 38.27 3.16
1657 2889 5.166398 GCAGAGATATTTTTGCAGCAGTTT 58.834 37.500 4.10 0.00 36.59 2.66
1658 2890 5.061808 GCAGAGATATTTTTGCAGCAGTTTG 59.938 40.000 4.10 0.00 36.59 2.93
1659 2891 6.154445 CAGAGATATTTTTGCAGCAGTTTGT 58.846 36.000 0.00 0.00 0.00 2.83
1660 2892 6.307318 CAGAGATATTTTTGCAGCAGTTTGTC 59.693 38.462 0.00 0.00 0.00 3.18
1661 2893 6.208204 AGAGATATTTTTGCAGCAGTTTGTCT 59.792 34.615 0.00 0.00 0.00 3.41
1662 2894 7.391554 AGAGATATTTTTGCAGCAGTTTGTCTA 59.608 33.333 0.00 0.00 0.00 2.59
1663 2895 7.885297 AGATATTTTTGCAGCAGTTTGTCTAA 58.115 30.769 0.00 0.00 0.00 2.10
1664 2896 8.526147 AGATATTTTTGCAGCAGTTTGTCTAAT 58.474 29.630 0.00 0.00 0.00 1.73
1665 2897 9.143631 GATATTTTTGCAGCAGTTTGTCTAATT 57.856 29.630 0.00 0.00 0.00 1.40
1666 2898 6.826893 TTTTTGCAGCAGTTTGTCTAATTC 57.173 33.333 0.00 0.00 0.00 2.17
1667 2899 5.512753 TTTGCAGCAGTTTGTCTAATTCA 57.487 34.783 0.00 0.00 0.00 2.57
1713 2945 2.832129 TCCGGCTACAAAGAAGATGTCT 59.168 45.455 0.00 0.00 38.69 3.41
1750 2982 0.471022 TGCCTAGACACCAGACACCA 60.471 55.000 0.00 0.00 0.00 4.17
1791 3023 3.057548 TCCGCTGCCTGCATTGTG 61.058 61.111 0.00 0.00 43.06 3.33
1845 3077 0.249911 GAAGCACCTTCCTCGTGTGT 60.250 55.000 0.00 0.00 34.71 3.72
1860 3092 3.047877 TGTCGCTCTCGTCGCTCA 61.048 61.111 0.00 0.00 36.96 4.26
1976 3208 4.742201 CGTGCCCCAGTCCAGACG 62.742 72.222 0.00 0.00 36.20 4.18
1983 3215 1.384989 CCCAGTCCAGACGCGTATCT 61.385 60.000 13.97 2.23 36.20 1.98
1990 3222 1.065701 CCAGACGCGTATCTGCTTACT 59.934 52.381 13.97 0.00 44.12 2.24
2247 3479 3.798954 GATGGCGAGCCTTCGGAGG 62.799 68.421 15.75 4.95 46.76 4.30
2343 3575 2.682836 GTTCTGAGAGGAGACAAGTGC 58.317 52.381 0.00 0.00 0.00 4.40
2345 3577 0.600557 CTGAGAGGAGACAAGTGCGT 59.399 55.000 0.00 0.00 0.00 5.24
2379 3611 4.697756 CCCAGCGGCTTCGTTCCA 62.698 66.667 0.00 0.00 36.07 3.53
2387 3619 1.140407 GGCTTCGTTCCATCTCGTCG 61.140 60.000 0.00 0.00 0.00 5.12
2606 3860 1.005394 GGGTCGGGTACTGTGTGTG 60.005 63.158 0.00 0.00 35.30 3.82
2662 3916 0.331278 CCAACACCCCTGCAATCCTA 59.669 55.000 0.00 0.00 0.00 2.94
2737 3991 3.461773 GAGGCCTGCGCTGACCTA 61.462 66.667 21.56 0.00 30.95 3.08
2746 4000 2.055042 CGCTGACCTAGGTGCCTCT 61.055 63.158 22.10 0.00 0.00 3.69
2844 4098 0.972471 CCTTTGGATCTGTTGGGCCC 60.972 60.000 17.59 17.59 0.00 5.80
2855 4109 3.598747 TTGGGCCCGGTGATGCAAT 62.599 57.895 19.37 0.00 0.00 3.56
2913 4167 2.267006 CCACGATGCTGAGCCACT 59.733 61.111 0.23 0.00 0.00 4.00
2916 4170 2.267006 CGATGCTGAGCCACTGGT 59.733 61.111 0.23 0.00 0.00 4.00
2921 4175 0.472044 TGCTGAGCCACTGGTAAACA 59.528 50.000 0.23 0.00 0.00 2.83
2922 4176 1.073763 TGCTGAGCCACTGGTAAACAT 59.926 47.619 0.23 0.00 0.00 2.71
2926 4180 2.371841 TGAGCCACTGGTAAACATCACT 59.628 45.455 0.00 0.00 0.00 3.41
2976 4230 3.005539 ACTGGCTGCTCGACCCAT 61.006 61.111 0.00 0.00 0.00 4.00
3224 4478 0.394899 CAAGAGGGGTCTGGCAATCC 60.395 60.000 0.00 0.00 0.00 3.01
3357 4630 2.505557 GGTCGACGCACCTAACCG 60.506 66.667 9.92 0.00 33.08 4.44
3381 4654 0.580104 GTTGTCCCTGTCGTTTGTCG 59.420 55.000 0.00 0.00 41.41 4.35
3416 4689 5.510520 CCCATGAGTAGCTTCTGTATCCTTC 60.511 48.000 0.00 0.00 0.00 3.46
3509 4782 2.676839 CCTGCTGTTATCTGTCTGCAAG 59.323 50.000 0.00 0.00 37.86 4.01
3593 4866 1.274728 AGTTCTGCTACTCACCTGCTG 59.725 52.381 0.00 0.00 0.00 4.41
3624 4897 1.615883 TGGTGGCATAATTGTTGCGTT 59.384 42.857 8.54 0.00 41.07 4.84
3666 4939 5.335583 CGATTGTGCCTAGTTCAATCCAAAA 60.336 40.000 17.80 0.00 42.21 2.44
3790 5063 3.388024 TGGATGACCTCAGGTTATACTGC 59.612 47.826 12.09 0.00 34.12 4.40
3820 5093 4.144297 ACATTCTGTGTATTTGCACTGGT 58.856 39.130 5.99 0.00 39.91 4.00
3884 5157 6.435430 TGAACATTAATCGGAGAACAATGG 57.565 37.500 9.94 0.00 42.39 3.16
3888 5161 2.496899 AATCGGAGAACAATGGCTGT 57.503 45.000 0.00 0.00 43.58 4.40
3952 5225 1.466025 TTCACGGGCGGAAGTACACT 61.466 55.000 0.00 0.00 0.00 3.55
4054 5327 0.608640 ACTCCATCCTTCGAGCGTTT 59.391 50.000 0.00 0.00 0.00 3.60
4183 5456 0.327924 ACCATGTGATTTCGGAGGCA 59.672 50.000 0.00 0.00 0.00 4.75
4231 5504 1.269988 CCGTATCTCATCCTGCACTGG 60.270 57.143 0.00 0.00 0.00 4.00
4311 5584 0.319728 AAGATCCGGATGGCGATCTG 59.680 55.000 24.82 10.41 43.48 2.90
4315 5588 1.338107 TCCGGATGGCGATCTGTAAT 58.662 50.000 15.45 0.00 33.55 1.89
4448 5721 1.152247 TCACACTGGAGGCAGAGGT 60.152 57.895 0.00 0.00 0.00 3.85
4509 5782 6.969342 CTGCTTTCTTGCGTTCAAAAGCAAT 61.969 40.000 21.58 0.00 46.64 3.56
4522 5795 0.035317 AAGCAATGGCACGACAGAGA 59.965 50.000 0.00 0.00 44.61 3.10
4726 5999 5.906772 TTTTCAGAAGAGGAAGTAAGGGT 57.093 39.130 0.00 0.00 0.00 4.34
4758 6031 3.257375 GGAAATTAACCCAAGAAAGGCGT 59.743 43.478 0.00 0.00 0.00 5.68
4799 6072 0.034059 CGCACTTCTTCCAGGTCTGT 59.966 55.000 0.00 0.00 0.00 3.41
4964 6237 8.378565 AGACCAATCAGTCTCATTTCTTTCTTA 58.621 33.333 0.00 0.00 43.76 2.10
5046 6319 0.244721 GCCCACTCAAAGTGCATTCC 59.755 55.000 1.49 0.00 44.63 3.01
5084 6357 3.187432 TGCACGACAATTTTATTCTCGCA 59.813 39.130 0.00 0.00 0.00 5.10
5135 6408 2.037385 AGATCCCTGCCCTCCTATTC 57.963 55.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 72 3.181522 GCTGTCTGCTCTGAATTTTCTCG 60.182 47.826 0.00 0.00 38.95 4.04
75 84 3.801698 TCTTCCATAATGCTGTCTGCTC 58.198 45.455 3.20 0.00 43.37 4.26
76 85 3.920231 TCTTCCATAATGCTGTCTGCT 57.080 42.857 3.20 0.00 43.37 4.24
77 86 3.186001 CGATCTTCCATAATGCTGTCTGC 59.814 47.826 0.00 0.00 43.25 4.26
78 87 4.375272 ACGATCTTCCATAATGCTGTCTG 58.625 43.478 0.00 0.00 0.00 3.51
79 88 4.679373 ACGATCTTCCATAATGCTGTCT 57.321 40.909 0.00 0.00 0.00 3.41
120 131 1.842465 AGCATGCCCTGGCCAAAAA 60.842 52.632 15.66 0.00 41.09 1.94
127 138 1.077285 TGTCATCAGCATGCCCTGG 60.077 57.895 15.66 2.07 34.76 4.45
331 347 4.899239 GTCAGGCGCTCCGATGGG 62.899 72.222 7.64 0.00 37.47 4.00
344 360 0.695347 AAGAAGGAGCCCTTGGTCAG 59.305 55.000 10.77 0.00 44.82 3.51
517 533 2.325761 CGAGTCCGTTGAAACCTGTAG 58.674 52.381 0.00 0.00 0.00 2.74
643 659 1.918293 ACCCTTCATGGCGAGGTCA 60.918 57.895 9.03 0.00 0.00 4.02
753 888 5.423015 GAAGCAACAGATCCATCTTGAGTA 58.577 41.667 0.00 0.00 34.22 2.59
802 937 1.003355 CAGAGGCCACGACAATGGT 60.003 57.895 5.01 0.00 42.28 3.55
816 951 0.901124 CCTCCACCTCCTTGTCAGAG 59.099 60.000 0.00 0.00 0.00 3.35
929 1064 2.744307 GAAGAACACGACGGTCGCCT 62.744 60.000 28.67 17.49 45.12 5.52
982 1117 4.845580 CGCCCTGCCTTGCTCGAT 62.846 66.667 0.00 0.00 0.00 3.59
1039 1174 6.147821 GTGATTATATCGAAGGTTGACATGGG 59.852 42.308 0.00 0.00 0.00 4.00
1047 1182 6.813649 CGATGATGGTGATTATATCGAAGGTT 59.186 38.462 0.00 0.00 39.60 3.50
1101 1236 2.668212 CTTCTTGCCGCCGGAACA 60.668 61.111 7.68 0.00 0.00 3.18
1113 1248 1.229209 TCTCCCCGTGAGCCTTCTT 60.229 57.895 0.00 0.00 41.18 2.52
1131 1266 1.398958 GCTCCGAGATGCCCTTCTCT 61.399 60.000 0.00 0.00 40.03 3.10
1480 1633 2.758737 GTCGTCGGGGATCCACCT 60.759 66.667 15.23 0.00 38.98 4.00
1531 1684 1.086696 CAACCAAGTACGGCCATCAG 58.913 55.000 2.24 0.00 0.00 2.90
1587 2818 3.161866 GCAACCCTTCCTGGATTTGTAA 58.838 45.455 0.00 0.00 38.35 2.41
1628 2860 2.760092 GCAAAAATATCTCTGCCCACCA 59.240 45.455 0.00 0.00 0.00 4.17
1629 2861 2.760092 TGCAAAAATATCTCTGCCCACC 59.240 45.455 0.00 0.00 33.78 4.61
1648 2880 4.470462 CTGTGAATTAGACAAACTGCTGC 58.530 43.478 0.00 0.00 0.00 5.25
1653 2885 5.934625 CAGTAGGCTGTGAATTAGACAAACT 59.065 40.000 0.00 0.00 37.92 2.66
1654 2886 5.122396 CCAGTAGGCTGTGAATTAGACAAAC 59.878 44.000 0.00 0.00 41.02 2.93
1655 2887 5.245531 CCAGTAGGCTGTGAATTAGACAAA 58.754 41.667 0.00 0.00 41.02 2.83
1656 2888 4.832248 CCAGTAGGCTGTGAATTAGACAA 58.168 43.478 0.00 0.00 41.02 3.18
1657 2889 4.471904 CCAGTAGGCTGTGAATTAGACA 57.528 45.455 0.00 0.00 41.02 3.41
1679 2911 2.918712 AGCCGGAATCTCCATTACTG 57.081 50.000 5.05 0.00 35.91 2.74
1791 3023 3.106407 GGTGTGTCGCTCTCGCAC 61.106 66.667 7.47 7.47 43.03 5.34
1845 3077 2.176055 GTTGAGCGACGAGAGCGA 59.824 61.111 0.00 0.00 41.64 4.93
1890 3122 0.324645 GGAGGGGTAGGGTGTCGTTA 60.325 60.000 0.00 0.00 0.00 3.18
1976 3208 2.159226 AGGTGTCAGTAAGCAGATACGC 60.159 50.000 0.00 0.00 0.00 4.42
1983 3215 0.321671 GCTGGAGGTGTCAGTAAGCA 59.678 55.000 0.00 0.00 34.89 3.91
2176 3408 2.111043 GGCCAGCAATAGCCGCTA 59.889 61.111 1.73 1.73 43.56 4.26
2372 3604 0.725686 GAGACGACGAGATGGAACGA 59.274 55.000 0.00 0.00 0.00 3.85
2379 3611 2.217750 CTCCATCAGAGACGACGAGAT 58.782 52.381 0.00 0.00 46.50 2.75
2606 3860 2.282040 AGTGGCAAGCTCCTGTGC 60.282 61.111 0.00 0.00 40.14 4.57
2662 3916 1.552792 GTAAGGTGCAGCTCTTCCTCT 59.447 52.381 20.46 3.89 0.00 3.69
2737 3991 2.433446 CCTTGCACAGAGGCACCT 59.567 61.111 0.00 0.00 44.86 4.00
2746 4000 2.194597 GGTGTGTCCCCTTGCACA 59.805 61.111 0.00 0.00 42.50 4.57
2780 4034 2.987547 CAACCCAGCAGGCCAGTG 60.988 66.667 5.01 0.00 40.58 3.66
2844 4098 3.366273 GCCCATTGTATATTGCATCACCG 60.366 47.826 0.00 0.00 0.00 4.94
2855 4109 2.224670 GGGTCATTCGGCCCATTGTATA 60.225 50.000 0.00 0.00 44.23 1.47
2913 4167 1.004277 GGGCCAGAGTGATGTTTACCA 59.996 52.381 4.39 0.00 0.00 3.25
2916 4170 3.517296 TTTGGGCCAGAGTGATGTTTA 57.483 42.857 6.23 0.00 0.00 2.01
2921 4175 2.622452 CCTCAATTTGGGCCAGAGTGAT 60.622 50.000 24.75 5.32 0.00 3.06
2922 4176 1.272092 CCTCAATTTGGGCCAGAGTGA 60.272 52.381 23.39 23.39 0.00 3.41
2926 4180 1.145900 TCCCCTCAATTTGGGCCAGA 61.146 55.000 6.23 1.42 43.26 3.86
2950 4204 1.886253 GAGCAGCCAGTCTCTCAGCA 61.886 60.000 0.00 0.00 0.00 4.41
2983 4237 4.019950 TCAATATCTGATGGCGATGATGGT 60.020 41.667 0.00 0.00 0.00 3.55
3127 4381 6.844388 TGTCAATCTTCCTTCCTAATAGCCTA 59.156 38.462 0.00 0.00 0.00 3.93
3224 4478 2.837291 CTCCTCTCCAGGCTCGGG 60.837 72.222 3.64 0.00 40.12 5.14
3357 4630 0.106149 AACGACAGGGACAACACCTC 59.894 55.000 0.00 0.00 35.78 3.85
3381 4654 3.879892 GCTACTCATGGGGAAACAAGATC 59.120 47.826 0.00 0.00 0.00 2.75
3416 4689 0.964358 AGACCCCGTACGTTCCAGAG 60.964 60.000 15.21 0.00 0.00 3.35
3593 4866 2.668550 GCCACCACGAGTCCCAAC 60.669 66.667 0.00 0.00 0.00 3.77
3624 4897 4.753516 ATCGTTACCACATCAGGATTCA 57.246 40.909 0.00 0.00 0.00 2.57
3666 4939 4.637534 CACAACCAGCTGCTATAAATGAGT 59.362 41.667 8.66 0.00 0.00 3.41
3804 5077 3.207265 AGTCACCAGTGCAAATACACA 57.793 42.857 0.00 0.00 43.23 3.72
3820 5093 1.425066 AGGGCAATGAGGTTGAAGTCA 59.575 47.619 0.00 0.00 40.37 3.41
3848 5121 8.893727 CCGATTAATGTTCAGGTTATTCTTCTT 58.106 33.333 0.00 0.00 0.00 2.52
3884 5157 0.865769 ATGAACCGACGAAACACAGC 59.134 50.000 0.00 0.00 0.00 4.40
3888 5161 3.394719 TCATTGATGAACCGACGAAACA 58.605 40.909 0.00 0.00 33.08 2.83
3952 5225 1.205655 CTCTCCTGCTCATTCGTCCAA 59.794 52.381 0.00 0.00 0.00 3.53
4026 5299 2.478292 GAAGGATGGAGTTGGGGTAGA 58.522 52.381 0.00 0.00 0.00 2.59
4054 5327 1.641192 TGGTCAGAGAGGCTAGAGGAA 59.359 52.381 0.00 0.00 0.00 3.36
4183 5456 1.134401 CATGCGTAGGGTCTGTTCCAT 60.134 52.381 0.00 0.00 0.00 3.41
4311 5584 5.123820 TCAAGCATACCAACAAGCTCATTAC 59.876 40.000 0.00 0.00 36.07 1.89
4315 5588 2.813754 GTCAAGCATACCAACAAGCTCA 59.186 45.455 0.00 0.00 36.07 4.26
4448 5721 4.740902 TCCCTGATCGAATCAATCCTAGA 58.259 43.478 0.00 0.00 39.11 2.43
4726 5999 4.601084 TGGGTTAATTTCCATTAAGGCGA 58.399 39.130 0.00 0.00 35.84 5.54
4758 6031 1.382009 TGAATCCATCCGGTCCCGA 60.382 57.895 7.42 0.00 42.83 5.14
4769 6042 0.035317 AGAAGTGCGCAGTGAATCCA 59.965 50.000 20.39 0.00 0.00 3.41
4799 6072 1.691219 GGCCTTGATCACCTCCCAA 59.309 57.895 0.00 0.00 0.00 4.12
4918 6191 4.406003 GTCTATAGTCCTTGGCCTCTTCAA 59.594 45.833 3.32 0.00 0.00 2.69
5046 6319 5.179368 TGTCGTGCAAAGATCTTCCTTTAAG 59.821 40.000 8.78 0.00 34.85 1.85
5084 6357 1.968017 CTGCCGTGTCATGCCTTGT 60.968 57.895 0.00 0.00 0.00 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.